kedro.extras.datasets.biosequence.BioSequenceDataSet

class kedro.extras.datasets.biosequence.BioSequenceDataSet(filepath, load_args=None, save_args=None, credentials=None, fs_args=None)[source]

Bases: kedro.io.core.AbstractDataSet

BioSequenceDataSet loads and saves data to a sequence file.

Example:

from kedro.extras.datasets.biosequence import BioSequenceDataSet
from io import StringIO
from Bio import SeqIO

data = ">Alpha\nACCGGATGTA\n>Beta\nAGGCTCGGTTA\n"
raw_data = []
for record in SeqIO.parse(StringIO(data), "fasta"):
    raw_data.append(record)

data_set = BioSequenceDataSet(filepath="ls_orchid.fasta",
                              load_args={"format": "fasta"},
                              save_args={"format": "fasta"})
data_set.save(raw_data)
sequence_list = data_set.load()

assert raw_data[0].id == sequence_list[0].id
assert raw_data[0].seq == sequence_list[0].seq

Attributes

BioSequenceDataSet.DEFAULT_LOAD_ARGS
BioSequenceDataSet.DEFAULT_SAVE_ARGS

Methods

BioSequenceDataSet.__init__(filepath[, …]) Creates a new instance of BioSequenceDataSet pointing to a concrete filepath.
BioSequenceDataSet.exists() Checks whether a data set’s output already exists by calling the provided _exists() method.
BioSequenceDataSet.from_config(name, config) Create a data set instance using the configuration provided.
BioSequenceDataSet.invalidate_cache() Invalidate underlying filesystem caches.
BioSequenceDataSet.load() Loads data by delegation to the provided load method.
BioSequenceDataSet.release() Release any cached data.
BioSequenceDataSet.save(data) Saves data by delegation to the provided save method.
DEFAULT_LOAD_ARGS = {}
DEFAULT_SAVE_ARGS = {}
__init__(filepath, load_args=None, save_args=None, credentials=None, fs_args=None)[source]

Creates a new instance of BioSequenceDataSet pointing to a concrete filepath.

Parameters:
  • filepath (str) – Filepath in POSIX format to sequence file prefixed with a protocol like s3://. If prefix is not provided, file protocol (local filesystem) will be used. The prefix should be any protocol supported by fsspec.
  • load_args (Optional[Dict[str, Any]]) – Options for parsing sequence files by Biopython SeqIO.parse().
  • save_args (Optional[Dict[str, Any]]) – file format supported by Biopython SeqIO.write(). E.g. {“format”: “fasta”}.
  • credentials (Optional[Dict[str, Any]]) – Credentials required to get access to the underlying filesystem. E.g. for GCSFileSystem it should look like {“token”: None}.
  • fs_args (Optional[Dict[str, Any]]) – Extra arguments to pass into underlying filesystem class constructor (e.g. {“project”: “my-project”} for GCSFileSystem), as well as to pass to the filesystem’s open method through nested keys open_args_load and open_args_save. Here you can find all available arguments for open: https://filesystem-spec.readthedocs.io/en/latest/api.html#fsspec.spec.AbstractFileSystem.open All defaults are preserved, except mode, which is set to r when loading and to w when saving.

Note: Here you can find all supported file formats: https://biopython.org/wiki/SeqIO

Return type:None
exists()

Checks whether a data set’s output already exists by calling the provided _exists() method.

Return type:bool
Returns:Flag indicating whether the output already exists.
Raises:DataSetError – when underlying exists method raises error.
classmethod from_config(name, config, load_version=None, save_version=None)

Create a data set instance using the configuration provided.

Parameters:
  • name (str) – Data set name.
  • config (Dict[str, Any]) – Data set config dictionary.
  • load_version (Optional[str]) – Version string to be used for load operation if the data set is versioned. Has no effect on the data set if versioning was not enabled.
  • save_version (Optional[str]) – Version string to be used for save operation if the data set is versioned. Has no effect on the data set if versioning was not enabled.
Return type:

AbstractDataSet
Returns:

An instance of an AbstractDataSet subclass.
Raises:

DataSetError – When the function fails to create the data set from its config.
invalidate_cache()[source]

Invalidate underlying filesystem caches.

Return type:None
load()

Loads data by delegation to the provided load method.

Return type:Any
Returns:Data returned by the provided load method.
Raises:DataSetError – When underlying load method raises error.
release()

Release any cached data.

Raises:DataSetError – when underlying release method raises error.
Return type:None
save(data)

Saves data by delegation to the provided save method.

Parameters:data (Any) – the value to be saved by provided save method.
Raises:DataSetError – when underlying save method raises error.
Return type:None